[Biojava-l] PSI-BLAST output processing

[Iddo Friedberg]

Hi All,

Apologies for cross-posting. Please email replies directly to me 
(idoerg@burnham.org), I
am not a resident of these lists.

I  would like to know the updated status of the various Bio*.org 
projects with regards to
PSI-BLAST processing. Could one person (or more) from biojava and 
bioperl answer the
following questions?  This is for a talk at BioCon 2003.

(BioCorba person: please go directly to question #6).

1) Do you have a PSI-BLAST parser? (OK, silly)

2) Filtering capabilities of the parser (e.g. include only sequences 
with a certain evalue
threshold)

3) Does your project have a multiple-sequence alignment class or somesuch?
(if not, skip to 4)
3.1) Can the MSA object be created from the PSI-BLAST parser output 
(/object instance)?
(Easy / Hard / No)
(a code snippet,  semi-functional, would be _highly_ appreciated, here 
and in questions of
similar vein).
3.2) Can the MSA be transferred as input to other programs?  (Easy / 
Hard / No)
3.3) Can you filter sequences from the MSA? What criteria?
3.4) Calculating conservation along an MSA column (Easy / Hard / No)

4) Do you have MSA profile / PSSM class, or somesuch?
(if not, skip to 5)
4.1) Creating a profile from a multiple sequence alignment: (Easy / Hard)
4.2) Filtering: same as 3.3

5) Anything else you might like to tell me about the PSI-BLAST output 
processing
capabilities of your projects would be grand.

6) (For BioCorba) Does BioCorba have a:
6.1) PSI-BLAST output object?
6.2) multiple sequence alignment object?
6.2) PSSM /profile object?
6.3) Anything else relevant to handling PSI-BLAST output?
6.4) IDL code snippets, if relevant, would be cool.

Many, many thanks in advance,

Iddo

-- 
Iddo Friedberg
The Burnham Institute
10901 N. Torrey Pines Rd.
La Jolla, CA 92037
USA
Tel: +1 (858) 646 3100 x3516
Fax: +1 (858) 646 3171